Improvement of critical components for rice mill is one of the issues constraining the development of rice milling industry. Unfortunately, the effect of configuration of rotating shaft on the flow behaviors, collision characteristics and even milling mechanisms of rice particles in a rice mill still remains poorly understood. In this work, motion of spherical particles in a lab-scale horizontal rice mill with different heights of convex ribs fixed on rotating shaft was simulated using the platform based on the discrete element method (DEM). Validity of the numerical model was confirmed by comparing individual resident time and power draw obtained from experiments with those from simulations. Effects of height of convex ribs on flow properties including the dispersion in the axial direction and the velocity gradient along the radial direction, and further on collision characteristics which are closely related to the rice milling mechanisms, were investigated from the quantitative and qualitative points of view. The results showed that the migration index characterizing dispersion degree and the mean effective collision number, increases to a maximum and then decreases with the increase in the height, while the difference index representing velocity gradient and the mean collision energy increases at first and then decreases with the increase in the height. This implies that the mean effective collision number describing uniformity of milling mainly depends on the degree of dispersion, whereas the mean collision energy representing intensity of milling primarily relies on the velocity gradient. Furthermore, an increase in the height within the accepted range leads to the larger total collision energy, which accelerates wear of rice grains. The results are useful for providing the theoretic guidelines to select appropriate parameters of rotating shaft for the design of stirrer mills.